collectsharedcommand.cpp

   1 /*
   2  *  collectsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "collectsharedcommand.h"
  11 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22
  23
  24 //**********************************************************************************************************************
  25
  26 CollectSharedCommand::CollectSharedCommand(){
  27         try {
  28                 globaldata = GlobalData::getInstance();
  29                 string fileNameRoot;
  30                 fileNameRoot = getRootName(globaldata->inputFileName);
  31                 format = globaldata->getFormat();
  32                 validCalculator = new ValidCalculators();
  33
  34                 //set users groups
  35                 setGroups();
  36
  37                 int i;
  38                 for (i=0; i<globaldata->Estimators.size(); i++) {
  39                         if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
  40                                 if (globaldata->Estimators[i] == "sharedchao") {
  41                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
  42                                 }else if (globaldata->Estimators[i] == "sharedsobs") {
  43                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
  44                                 }else if (globaldata->Estimators[i] == "sharedace") {
  45                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
  46                                 }else if (globaldata->Estimators[i] == "sharedjabund") {
  47                                         cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
  48                                 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
  49                                         cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
  50                                 }else if (globaldata->Estimators[i] == "sharedjclass") {
  51                                         cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
  52                                 }else if (globaldata->Estimators[i] == "sharedsorclass") {
  53                                         cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
  54                                 }else if (globaldata->Estimators[i] == "sharedjest") {
  55                                         cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
  56                                 }else if (globaldata->Estimators[i] == "sharedsorest") {
  57                                         cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
  58                                 }else if (globaldata->Estimators[i] == "sharedthetayc") {
  59                                         cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
  60                                 }else if (globaldata->Estimators[i] == "sharedthetan") {
  61                                         cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
  62                                 }
  63                         }
  64                 }
  65
  66                 //reset calc for next command
  67                 globaldata->setCalc("");
  68
  69         }
  70         catch(exception& e) {
  71                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  72                 exit(1);
  73         }
  74         catch(...) {
  75                 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  76                 exit(1);
  77         }
  78
  79 }
  80
  81 //**********************************************************************************************************************
  82
  83 CollectSharedCommand::~CollectSharedCommand(){
  84         delete order;
  85         delete input;
  86         delete cCurve;
  87         delete read;
  88 }
  89
  90 //**********************************************************************************************************************
  91
  92 int CollectSharedCommand::execute(){
  93         try {
  94                 int count = 1;
  95
  96                 //if the users entered no valid calculators don't execute command
  97                 if (cDisplays.size() == 0) { return 0; }
  98
  99                 if (format == "sharedfile") {
 100                         read = new ReadPhilFile(globaldata->inputFileName);
 101                         read->read(&*globaldata);
 102
 103                         input = globaldata->ginput;
 104                         order = input->getSharedOrderVector();
 105                 }else {
 106                         //you are using a list and a groupfile
 107                         read = new ReadPhilFile(globaldata->inputFileName);
 108                         read->read(&*globaldata);
 109
 110                         input = globaldata->ginput;
 111                         SharedList = globaldata->gSharedList;
 112                         order = SharedList->getSharedOrderVector();
 113                 }
 114                 set<string> orderList;
 115
 116                 while(order != NULL){
 117                         orderList.insert(order->getLabel());
 118                         if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 119                                 //create collectors curve
 120                                 cCurve = new Collect(order, cDisplays);
 121                                 convert(globaldata->getFreq(), freq);
 122                                 cCurve->getSharedCurve(freq);
 123
 124                                 delete cCurve;
 125
 126                                 cout << order->getLabel() << '\t' << count << endl;
 127                         }
 128
 129                         //get next line to process
 130                         if (format == "sharedfile") {
 131                                 order = input->getSharedOrderVector();
 132                         }else {
 133                                 //you are using a list and a groupfile
 134                                 SharedList = input->getSharedListVector(); //get new list vector to process
 135                                 if (SharedList != NULL) {
 136                                         order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
 137                                 }else {
 138                                         break;
 139                                 }
 140                         }
 141
 142                         count++;
 143                 }
 144                 set<string>::iterator i;
 145                 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
 146                         if(orderList.count(*i) == 0)
 147                                 cout << "'" << *i << "'" << " is not a valid label.\n";
 148                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 149
 150                 //reset groups parameter
 151                 globaldata->Groups.clear();  globaldata->setGroups("");
 152
 153                 return 0;
 154         }
 155         catch(exception& e) {
 156                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159         catch(...) {
 160                 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163 }
 164
 165
 166 //**********************************************************************************************************************
 167 void CollectSharedCommand::setGroups() {
 168         try {
 169                 //if the user has not entered specific groups to analyze then do them all
 170                 if (globaldata->Groups.size() != 0) {
 171                         if (globaldata->Groups[0] != "all") {
 172                                 //check that groups are valid
 173                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 174                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 175                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 176                                                 // erase the invalid group from globaldata->Groups
 177                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 178                                         }
 179                                 }
 180
 181                                 //if the user only entered invalid groups
 182                                 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
 183                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 184                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 185                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 186                                         }
 187                                 }
 188                         }else{//user has enter "all" and wants the default groups
 189                                 globaldata->Groups.clear();
 190                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 191                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 192                                 }
 193                                 globaldata->setGroups("");
 194                         }
 195                 }else {
 196                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 197                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 198                         }
 199                 }
 200
 201         }
 202         catch(exception& e) {
 203                 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206         catch(...) {
 207                 cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210
 211 }
 212 /***********************************************************/
 213